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- PDB-3vyb: Crystal structure of methyl CpG binding domain of MBD4 in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vyb | ||||||
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Title | Crystal structure of methyl CpG binding domain of MBD4 in complex with the 5mCG/hmCG sequence | ||||||
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![]() | HYDROLASE/DNA / ![]() ![]() | ||||||
Function / homology | ![]() Cleavage of the damaged pyrimidine / Displacement of DNA glycosylase by APEX1 / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Otani, J. / Arita, K. / Kato, T. / Kinoshita, M. / Ariyoshi, M. / Shirakawa, M. | ||||||
![]() | ![]() Title: Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4 Authors: Otani, J. / Arita, K. / Kato, T. / Kinoshita, M. / Kimura, H. / Suetake, I. / Tajima, S. / Ariyoshi, M. / Shirakawa, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.2 KB | Display | ![]() |
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PDB format | ![]() | 52.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3vxvSC ![]() 3vxxC ![]() 3vyqC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | ![]() Mass: 7829.089 Da / Num. of mol.: 1 / Fragment: methyl CpG binding domain, UNP residues 69-136 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9Z2D7, ![]() |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 4263.809 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 4341.827 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 3 types, 73 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ACT / ![]() |
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#5: Chemical | ChemComp-EDO / ![]() |
#6: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.67 Å3/Da / Density % sol: 66.53 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 8% PEG 1500, 0.1M sodium acetate, 0.1M sodium cacodylate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 8, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.19→50 Å / Num. obs: 11517 / % possible obs: 89.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Biso Wilson estimate: 48.25 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.19→2.27 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.317 / Num. unique all: 701 / % possible all: 54.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3VXV Resolution: 2.4→34.7 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.43 / σ(F): 0 / Phase error: 24.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.965 Å2 / ksol: 0.329 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.75 Å2 / Biso mean: 47.8984 Å2 / Biso min: 22.03 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→34.7 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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